Zinc in PDB 7orv: Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239

Protein crystallography data

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239, PDB code: 7orv was solved by V.O.Talibov, F.Kozielski, C.Sele, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, W.Knecht, S.Z.Fisher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.66 / 1.95
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.236, 107.236, 107.236, 90, 90, 90
R / Rfree (%) 17 / 20.2

Other elements in 7orv:

The structure of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 (pdb code 7orv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239, PDB code: 7orv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7orv

Go back to Zinc Binding Sites List in 7orv
Zinc binding site 1 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:45.5
occ:1.00
NE2 A:HIS83 2.1 47.2 1.0
SG A:CYS77 2.3 45.5 1.0
SG A:CYS74 2.3 43.7 1.0
SG A:CYS90 2.3 46.8 1.0
CD2 A:HIS83 3.1 47.9 1.0
CE1 A:HIS83 3.1 51.4 1.0
CB A:CYS74 3.2 39.5 1.0
CB A:CYS90 3.3 51.3 1.0
CB A:CYS77 3.4 45.5 1.0
N A:CYS77 3.6 40.4 1.0
CA A:CYS77 4.0 42.7 1.0
ND1 A:HIS83 4.2 48.4 1.0
CG A:HIS83 4.2 49.9 1.0
O A:HOH372 4.4 56.2 1.0
O A:HOH379 4.4 65.9 1.0
CA A:CYS90 4.5 48.0 1.0
CB A:TYR76 4.5 43.7 1.0
C A:TYR76 4.6 41.8 1.0
CA A:CYS74 4.6 38.5 1.0
CA A:TYR76 4.9 42.7 1.0
CB A:LYS93 5.0 58.1 1.0
C A:CYS74 5.0 37.7 1.0
N A:TYR76 5.0 41.7 1.0

Zinc binding site 2 out of 2 in 7orv

Go back to Zinc Binding Sites List in 7orv
Zinc binding site 2 out of 2 in the Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non-Structural Protein 10 (NSP10) From Sars Cov-2 in Complex with Fragment VT00239 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:81.1
occ:1.00
SG A:CYS117 2.1 74.3 1.0
SG A:CYS128 2.1 74.0 1.0
SG A:CYS120 2.4 72.6 1.0
SG A:CYS130 2.6 94.3 1.0
CB A:CYS117 2.9 71.5 1.0
CB A:CYS130 3.4 90.4 1.0
CB A:CYS128 3.4 77.5 1.0
CB A:CYS120 3.6 70.5 1.0
N A:CYS120 3.8 79.3 1.0
CA A:CYS128 4.1 75.0 1.0
N A:CYS130 4.3 89.3 1.0
CA A:CYS120 4.3 71.5 1.0
CA A:CYS117 4.4 68.2 1.0
CB A:VAL119 4.5 88.2 1.0
CA A:CYS130 4.5 90.0 1.0
N A:SER129 4.6 91.6 1.0
C A:CYS128 4.7 82.3 1.0
C A:CYS117 4.9 74.3 1.0
C A:VAL119 4.9 82.7 1.0

Reference:

F.Kozielski, C.Sele, V.O.Talibov, J.Lou, D.Dong, Q.Wang, X.Shi, M.Nyblom, A.Rogstam, T.Krojer, Z.Fisher, W.Knecht. Identification of Fragments Binding to Sars-Cov-2 NSP10 Reveals Ligand-Binding Sites in Conserved Interfaces Between NSP10 and NSP14/NSP16 Rsc Chem Biol 2021.
ISSN: ESSN 2633-0679
DOI: 10.1039/D1CB00135C
Page generated: Fri Nov 5 16:55:58 2021

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